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Yorodumi- EMDB-36746: CryoEM structure of the Salmonella effector inositol phosphate ph... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36746 | |||||||||
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Title | CryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Type III secretion system / inositol phosphate phosphatase / bacteria effector / LIPID BINDING PROTEIN | |||||||||
Function / homology | Function and homology information negative regulation of signaling / symbiont-containing vacuole / regulation of protein kinase activity / lipid phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / positive regulation of DNA replication / molecular function activator activity / cell periphery / negative regulation of cell growth Similarity search - Function | |||||||||
Biological species | Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||
Authors | Jiang WX / Cheng XQ / Wu M / Ma LX | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of the Salmonella effector inositol phosphate phosphatase SopB Authors: Jiang WX / Cheng XQ / Wu M / Ma LX / Xing Q | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36746.map.gz | 207.6 MB | EMDB map data format | |
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Header (meta data) | emd-36746-v30.xml emd-36746.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36746_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_36746.png | 44.8 KB | ||
Filedesc metadata | emd-36746.cif.gz | 5.3 KB | ||
Others | emd_36746_half_map_1.map.gz emd_36746_half_map_2.map.gz | 391.5 MB 391.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36746 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36746 | HTTPS FTP |
-Validation report
Summary document | emd_36746_validation.pdf.gz | 910.8 KB | Display | EMDB validaton report |
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Full document | emd_36746_full_validation.pdf.gz | 910.3 KB | Display | |
Data in XML | emd_36746_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | emd_36746_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36746 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36746 | HTTPS FTP |
-Related structure data
Related structure data | 8jzlMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36746.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.566 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36746_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36746_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homohexamer of inositol phosphate phosphatase SopB
Entire | Name: Homohexamer of inositol phosphate phosphatase SopB |
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Components |
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-Supramolecule #1: Homohexamer of inositol phosphate phosphatase SopB
Supramolecule | Name: Homohexamer of inositol phosphate phosphatase SopB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) |
-Macromolecule #1: Inositol phosphate phosphatase SopB
Macromolecule | Name: Inositol phosphate phosphatase SopB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO EC number: Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
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Source (natural) | Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) |
Molecular weight | Theoretical: 55.05268 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: QHQKASNHSL HNLYNLQRDL LTVAATVLGK QDPVLTSMAN QMELAKVKAD RPATKQEEAA AKALKKNLIE LIAARTQQQD GLPAKEAHR FAAVAFRDAQ VKQLNNQPWQ TIKNTLTHNG HHYTNTQLPA AEMKIGAKDI FPSAYEGKGV CSWDTKNIHH A NNLWMSTV ...String: QHQKASNHSL HNLYNLQRDL LTVAATVLGK QDPVLTSMAN QMELAKVKAD RPATKQEEAA AKALKKNLIE LIAARTQQQD GLPAKEAHR FAAVAFRDAQ VKQLNNQPWQ TIKNTLTHNG HHYTNTQLPA AEMKIGAKDI FPSAYEGKGV CSWDTKNIHH A NNLWMSTV SVHEDGKDKT LFCGIRHGVL SPYHEKDPLL RHVGAENKAK EVLTAALFSK PELLNKALAG EAVSLKLVSV GL LTASNIF GKEGTMVEDQ MRAWQSLTQP GKMIHLKIRN KDGDLQTVKI KPDVAAFNVG VNELALKLGF GLKASDSYNA EAL HQLLGN DLRPEARPGG WVGEWLAQYP DNYEVVNTLA RQIKDIWKNN QHHKDGGEPY KLAQRLAMLA HEIDAVPAWN CKSG KDRTG MMDSEIKREI ISLHQTHMLS APGSLPDSGG QKIFQKVLLN SGNLEIQKQN TGGAGNKVMK NLSPEVLNLS YQKRV GDEN IWQSVKGISS LITS UniProtKB: Inositol phosphate phosphatase SopB |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |